domains / families / science / scikit-bio

scikit-bio

combined

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis. A Python bioinformatics toolkit for sequence, phylogeny, and microbiome/community-ecology analysis; use it when you need to compute diversity/ordination/statistics from biological data and standard formats (FASTA/FASTQ/Newick/BIOM).

When to use

• Works with biological sequences (DNA, RNA, protein)
• Needs to read/write biological file formats (FASTA, FASTQ, GenBank, Newick, BIOM, etc.)
• Performs sequence alignments or searches for motifs
• Constructs or analyzes phylogenetic trees
• Calculates diversity metrics (alpha/beta diversity, UniFrac distances)
• Performs ordination analysis (PCoA, CCA, RDA)
• Runs statistical tests on biological/ecological data (PERMANOVA, ANOSIM, Mantel)
• Analyzes microbiome or community ecology data

Skill page

Conflict

The copies overlap heavily on the high-level capabilities (sequences, alignment, trees, diversity, ordination, PERMANOVA), but they disagree on the concrete API to use. K-Dense-AI targets scikit-bio 0.7.4 and documents the new pair_align / pair_align_nucl / pair_align_prot API, explicitly noting that the SSW wrappers were removed. Vibe-Skills and OpenClaw-Medical-Skills still instruct the agent to use local_pairwise_align_ssw and StripedSmithWaterman, which are deprecated/removed in the newer version. aipoch/medical-research-skills targets an older version (>=0.6.0) and provides a different, more end-to-end example workflow. Crowning one copy would hide the version-specific API differences and the alternative workflow style.